Mass Effect:How He Fought Agaisnt a Metal God
by marthw
Summary: This is the story of how Commander Shepard fought off the effects of indoctrination, and continued the fight against the Reapers.


Mass Effect:How He Fought Against a Metal God

So this is my first fan fiction. Open to reviews and feedback please.

A tale of how Commander Shepard refused to give into the powerful mind controlling effects of the Reapers and stayed true to his mission.

Extended Cut, Destroy Ending, High EMS, romanced Liara, Renegade Path

Chapter 1

Shepard slowly inched up the ramp, his injured leg slowing him down, slightly dragging behind him. Only one thing racing through his mind, reaching the power conduit in front of him.

As he progressed towards its, he could hear the voice of the Illusive Man in the back of his head, one last ditch effort to try and sway him, "_No Shepard, the only way is to control them . . ._", as Shepard fought to keep the Illusive Man out of his head, thoughts of his crew, his friends, and his loved ones, began to overpower his voice and gave him the courage to resist.

He was almost to the end of the platform, his arm was to injured to steadily aim his hand as he raised the pistol. He thought of Anderson's last words to him, "_I'm . . . proud of you . . ._". He fired into the glass shield protecting the power coupling. Garrus's voice came into his mind, "_See you at the bar Shepard . . ._". The glass shattered, exposing the hardware underneath it, Shepard's resolve strengthened and his pace quickened into a fast stride, determination coursing through every vein and artery in his body. His thoughts came to be centered on Liara, the blue skinned alien that had come to be his lover, her sweet sounding words seemed to reverberate throughout his skull, drowning out everything else, "_I guess the little blue children will be disappointed I didn't have a speech ready_ . . .". Shepard looked away for a moment, towards the battle that raged outside the Citadel.

An alliance dreadnaught was hit port side by the main gun of a Reaper, almost instantly, the dreadnaught exploded into an orange and red fireball. Shepard looked back to the exposed power conduit with rage in his eyes, " Take this you Reaper bastards", he muttered as he raised his weapon, his arm didn't shake this time as he aimed down the sights. He fired. Then … darkness consumed him.

The rushing noise made by the transport beam to the Citadel was deafening. It made it impossible to

hear anyone over their shortwave communicators. Commands from the forward operating base(FOB) were going unheeded, and Hammer was being devastated after the Normandy had gone back to do an emergency pickup.

No one knew what was going on, only that Hammer team had failed to make it to the Citadel beam once Harbinger had detached itself from the raging space battle. Once Harbinger had decimated the combined forces of Hammer, he deactivated the beam. The terrible whooshing sound that it had made was ended, and only the sounds of screams and explosions could be heard as the Reaper took off. As it rose through the atmosphere, the Normandy appeared from behind the rubble of skyscrapers in the London skyline. As they prepared to touch down on the narrow strip leading up to the beam, husks began to emerge from the rubble surrounding the no mans land. Alliance marines were suiting up in the hanger bay of the Normandy, preparing to combat any hostiles as the team prepared to find Shepard's body and see if there was a way to still get to the Citadel from Earth's surface.

When Shepard had been hit with Harbingers beam, any and all life signs that were monitored through his armor by EDI back on the Normandy immediately went critical and then ceased altogether. Joker and the rest of the crew had refused to leave the planet until they could figure out what happened to Shepard, they had tried to assist Hammer as much as possible after the pickup, but had to fall back when all air support was downed by Harbinger.

Everyone in the hanger felt the landing gear absorb the shock from the landing. Steve Cortez opened the hanger bay doors and the marines rushed down the gangway to engage hostiles and secure the landing zone. The husks that had been gathering around the Normandy as it was preparing to land charged as soon as they saw light emanating from the open doors of the hanger. They were no match for the well trained marines in tight formation. As the marines took down the last husk, Garrus and Liara, who were both freshly healed with large doses of medigel, along with Tali, Vega, Javik, and Kaiden, ran out and immediately began searching for anything that could help them find the commander.

"There, that's were we were life-lighted out", yelled Garrus.

"Then that's were we'll find Shepard", Tali replied.

And along with the marines from the Normandy they spread out and began to march down to the last place that any of them had seen the brave Commander John Shepard.

Chapter 2

They pushed and pulled at the charred pieces of tanks and gunships that had fallen from the skies during the rush to the beam, desperately searching for the man who had brought an entire galaxy together. They were searching through rubble for approximately 15 minutes until they came across the scorch mark Harbinger had made shooting at Shepard. Another five until they finally found his body.

When they finally found him, his body was sprawled out, spreadeagled. His face bruised, bloody, and the left side mangled by shrapnel starting at his eye and going to his ear. His armor was barely intact. His kinetic barriers had been the first to go from the blast fired by the Reaper general. With nothing to stop projectiles, and being knocked unconscious, he couldn't protect himself or dodge shrapnel. His left leg and lower abdomen had been pierced by larger pieces of shrapnel form the blast and he had lost three finger on his left hand.

"Oh god, is he . . .", Liara uttered as she looked down at the man she loved.

Kaiden knelt down next to the commander and placed two fingers on his neck.

"I don't believe it" Kaiden whispered, "He's got a pulse, barely, but he's still with us. Liara, look at me, god dammit Liara, I need you to focus now!"

The asari had begun to break down and was covering her eyes.

"I need you to get a hold of yourself and help me transport him", Kaiden said as Liara finally looked at him, "You keep him secured with stasis, and I'll move his body, OK."

Liara looked down at Shepard, then back to Kaiden, "OK, lets get him back to the Normandy."

Liara walked over next to Shepard, starting to glow blue as she moved. She whipped her hand forward and a bluish white light came over Shepard's body, immediately immobilizing him. Kaiden came up on the other side, also glowing blue and brought both hands up. Shepards body rose off the ground and began moving to were the Normandy was grounded. Meanwhile Tali, Javik and Garrus, were examining were the beam had been shooting up to the Citadel.

"What do you think Garrus", asked Tali.

"I don't think we can use the beam anymore. Harbinger must have deactivated it when he realized the threat it presented." Garrus replied.

"We must find an alternative means of deploying the Crucible then. I will have my vengeance against

the machines" Javik said to them.

Vega ran over to them to let them know they were moving the Commander. They all started back to the ship, reuniting with the marines who had detached and searched in another location. Garrus sent a message to Joker back at the Normandy.

"Joker, we found the commander but the beam is a no go. We have to figure something else out."

Joker's face popped up on Garrus's omnitool, " Copy Garrus, Try and get back to the Normandy ASAP. We just picked up a distress signal from the FOB. Anderson and Coates fell back to it when Hammer failed, but when they got back, the base was overrun. Now they're radioing for pick up and Reaper forces are closing in. Fast."

Garrus looked down at Joker, "We read you Joker, we'll move as fast as we can. Just have Dr. Chakwas waiting for us down in the hanger. Shepard is in pretty bad shape. Over and out."

Garrus looked around at the ground team, "Alright people, we need to be at the Normandy five minutes ago. Double time! Lets move!"

Chapter 3

The rescue team came up on the Normandy, the alliance marines forming a wall to protect Shepard's and his crew, as they escorted them back to the ship. All of a sudden, a group of husks seemingly came out of nowhere and took one of the marines by surprise.

He was screaming as the husks began tearing his armor off to get to his flesh. The rescue team looked back to see that the husks had overwhelmed him. Garrus and Vega looked at one another. Vega whipped out his shotgun and switched to the under-barrel. He fired a carnage round into the mass of husks. As they exploded into a fiery mess of burning flesh and bloody cybernetic parts, a couple not hit by the blast were picked off by Garrus's rifle.

"Nice shot Scars", Vega yelled out to Garrus.

"Keep moving!", Garrus reiterated.

The group finally made it back to the Normandy. As they moved up the ramp. They were greeted by Dr. Chakwas and the Normandy's med team.

Chakwas looked down at Shepard as Kaiden brought him past her, " Get him up to the med bay at once, we need to determine the extent of his injuries."

They loaded him into the elevator and brought him into the med bay to get him secured, and to immediately begin tests and evaluations.

"We'll need some time to get him situated, from what I understand you all need to head back down to the hanger to prep for the Admiral's extraction", she dictated to the crew.

"You heard the woman, everyone back down to the hanger, let's go", Garrus yelled at his crewmates.

They loaded ammo into their weapons, checked and then double checked their armor specs as the Normandy flew back to the FOB.

Joker announced over the intercom, "Touching down at the FOB. Extraction team be prepped and ready."

Cortez yelled at the crew, "Hanger bay doors opening now."

The emergency lights flashed around the hanger as the door opened. Immediately they were met with a barrage of gun fire. Two marines that were coming down the ramp were cut down before they even reached the bottom of it. Liara threw up a biotic barrier to try and protect everyone leaving the ship as best she could after that.

Vega and Javik lead the charge as the rest of the extraction team followed them down the ramp. They moved quickly from cover to cover. Cutting down marauder after marauder and a countless number of husks as they moved deeper into the smoking remains of the FOB.

When they found Andersen's shuttle it had crashed landed onto the makeshift landing pad constructed in the middle of a roundabout. Major Coates and Andersen, along with their pilot and two marines, were pinned down next to the wreckage. Garrus split off with a handful of marines and flanked the Reapers forces that had them pinned down. When the last Cannibal fell, the survivors of the downed shuttle met up with the extraction team.

Anderson, "What happened, what are all of you doing planet-side?"

Vega looked at Anderson, "Something happened to Shepard, we doubled back to find him. He's in pretty bad shape."

Anderson glanced at Coates, then back to the extraction team, "We figured something went wrong, we lost all contact with the squads making a dash to the beam. Then we fell back to the FOB when we heard that the Reapers were making a push here. By the time we got back though, the FOB had already fallen and the Reaper's were established in force here. They shot us down and we've been radioing for pickup since", Anderson explained as they made their way out of the roundabout and down the road the pickup team had come through. As they moved back to the Normandy, taking as many Reapers out as they could, Anderson was contacted by Hackett.

Hackett, "Anderson, report. What's going on down there. Has Hammer hit the beam yet?"

Anderson, "Hackett, our forces were pushed back. Hammer is in shambles and the FOB is gone. The beam has been deactivated and we have no way of getting to the Citadel from Earth. Whats going on with Shield and the Crucible?"

Hackett, "As of now, we're holding our own. We've kept the Crucible out of harm's way, but we don't know for how much longer, especially if there's no way to get to the Citadel from Earth or space. We need to regroup and figure out the next move."

Anderson,"We'll keep you informed if an opportunity presents itself down here. But don't hold your breath Steve. Anderson out."

Hackett, "Understood David, Hackett out."

As the extraction team neared the Normandy, the ground started to shake around them. As they looked around to try and figure out what was going on, a Brute burst out from behind a brick wall they were passing.

"Brute! Everyone take cover", Tali yelled, as she aimed her shotgun and began firing in its direction.

Major Coates was unable to take cover, and had to dodge as the Brute lowered its shoulder and charged him. As he picked himself off the ground, he saw that the Brute had already turned around and was charging again. As he reached his feet, it slammed into him and pinned him to a car. The extraction team fired at the Brute, but could not take it down. Husks and marauders began to spill out from the brick wall that the Brute had come from, forcing the extraction team to move back to a row of overturned cars for cover. Major Coates turned his head and saw the Reaper troops coming, and with his free arm reached down to his belt to grab a grenade. Without hesitation, he pulled the pin.

"Suck on this you fucking monster!", he yelled as he stuck it into the open mouth of the Brute.

Anderson and the extraction team watched as the Brute exploded and took out most of the Reaper troops that had followed it. Anderson looked on and with a sad realization it dawned on him what the Major had done. After they took out the last of the Reaper troops, they picked up their gear and moved as quick as they could, all silently thanking the Major for his sacrifice.

Chapter 4

As the extraction team headed up the ramp of the Normandy, Anderson brought Joker up on vidcomm.

"Joker", Anderson said, "Get us in the air and to the rendezvous point. We need to regroup with whats left of Hammer."

"Understood Admiral", Joker responded.

They moved up the ship and headed towards the med bay. The ground team that was with Shepard during the push to the beam informed Anderson of what had occurred.

"As we were heading to the beam, Liara and I were injured," Garrus explained to Anderson in the elevator. "Shepard called in the Normandy to air lift us out, about three minutes after that his vitals flat lined from the monitors in his armor."

"We couldn't land because Harbinger was taking out everything stationary," Liara explained, "So we provided air support and hung back till we could."

Anderson sighed and then looked at the two of them,"I don't blame you all for not falling back in line with Shield, it was probably for the best."

As they arrived on the living quarters deck, Dr. Chakwas saw them and came out of the med bay to meet them.

"Hello Admiral Anderson, Garrus, . . . Liara." She nodded curtly at them as she said their names.

"Commander Shepard is still alive but his injuries are extensive. We've repaired what we could with medi-gel, and the cybernetic implants installed by Cerberus have aided in the healing process.

Physically he is almost completely healed. However, we noticed some irregular brain wave activity during a CT scan of the commanders brain."

"What do you mean doctor?", Anderson asked.

"We were checking to see if he suffered any head trauma, only we found some serious degenerative neural scarring that was not there previously. We have a theory about what caused it, only . . . "

"What is it Dr.?" Garrus asked.

"Indoctrination, the scarring is possibly a side effect of indoctrination" Karin told them.

Anderson, Liara, and Garrus stood absolutely dumbfounded.

"Not possible," Anderson yelled, "there's no way in hell the Commander is indoctrinated, we would have been able to see it. Not to mention he would have been actively trying to sabotage the war effort. Shepard has been the unifying force behind our efforts."

Chakwas looked at Anderson waiting for him to finish before she responded to the Admiral, "Correct Admiral, Commander Shepard has never done anything to compromise the war effort, the scarring that is present now is indicative of intense pressure, put on the mind in a very small window of time. Possibly a few days, maybe even a few hours. I believe the fact that Shepard has not awoken yet even though his body is almost healed, shows that he is resisting the attempt to take over his mind."

"So what now?" Garrus asked the Dr.

"We have done all we can physically do for him", Chakwas explained, "now its up to the Commander."

"I'd like to see him please," Liara squeaked out, barely able to speak as she dealt with the frightening truth.

Chakwas looked at Liara, "Of course dear, come with me. I'll take you to him."

As Liara and the Dr. headed into the med bay, Garrus turned to Anderson, "So what now, what do we do?"

"Nothing has changed, we make for the rendezvous point, and figure out some kind of counterattack" Anderson said, with forced courage, "until then we just focus on staying alive."

Garrus thought long and hard about the next thing he wanted to say, "What do we do if Shepard wakes up and he's been indoctrinated?"

Anderson took a second to mull over the question before he looked at Garrus and said, "We'll do what has to be done."

Garrus nodded and headed back down to the elevator to alert the rest of the crew where they were headed. Anderson looked up as Garrus turned around the corner, a thought coming to mind.

Anderson caught up to Garrus as he was entering the elevator and said, "Garrus, wait! Don't let the rest of the crew know about Shepard."

Garrus gave him a look of understanding, and nodded his head once again as the elevator doors closed shut.


End file.
